If you rename your old unity folder to something (ie: "Unity 4.6") you can install the new version side-by-side. If you have a folder called "Unity" already though, the old version will be overwritten.

And yes, I've tried the WebGL demo on both of my latest Unity games on FGL (Vine Time, Move That Box!), it works wonderfully! Incredibly easy too, just like deploying to any other unity platform. You simply choose the platform you want, hit "Build", and voilà!

On Mar 03, 2015, TubeMice said:

Oh yes, @Dmeville, did you already tried it? Did you tried deploy to WebGL? How's that work?

I wonder if I need to uninstall Unity4, or install Unity5 to a separate location

There's a few API changes, mostly properties that were on gameobjects (like gameobject.rigidbody, gameobject.renderer) now have to be accessed via gameobject.GetComponent<Renderer>. When you open a 4.x project in unity 5 though, it automatically runs an API updater and makes most of these changes for you.